A comparison of alternative mRNA splicing in the CD4 and CD8 T cell lineages. (May 2021)

• Record Type: Journal Article
• Authors: Liu, Xin; Andrews, Matthew V.; Skinner, Jarrod P.; Johanson, Timothy M.; Chong, Mark M.W.
• Is Part Of: Molecular immunology. Volume 133(2021)
• Page Start: 53
• Page End: 62
• Publication Date: 2021-05
• Subjects: Alternative mRNA splicing -- CD4 versus CD8 T cell lineages -- Transcriptomics -- High throughput sequencing -- Illumina -- PacBio; Immunochemistry -- Periodicals; Molecular biology -- Periodicals; Immunochemistry -- Periodicals; Allergy and Immunology -- Periodicals; Molecular Biology -- Periodicals; Immunochimie -- Périodiques; Biologie moléculaire -- Périodiques; Immunochemistry; Molecular biology; Periodicals; Electronic journals; 571.96
• DOI: 10.1016/j.molimm.2021.02.009
• Languages: English
• ISSNs: 0161-5890

Abstract

Highlights: Integrating short and long RNA-seq data is effective for mapping and quantifying alternative mRNA splicing. Short-read alone is ineffective for assembling alternatively spliced mRNAs, while long-read is inaccurate for quantification. Overall splicing diversity is similar between CD4 and CD8 T cells, but some isoforms are preferentially used by a lineage. We describe in detail two genes that produce alternative spliced isoforms that differ between CD4 and CD8 T cells. Abstract: T cells can be subdivided into a number of different subsets that are defined by their distinct functions. While the specialization of different T cell subsets is partly achieved by the expression of specific genes, the overall transcriptional profiles of all T cells appear very similar. Alternative mRNA splicing is a mechanism that facilitates greater transcript/protein diversity from a limited number of genes, which may contribute to the functional specialization of distinct T cell subsets. In this study we employ a combination of short-read and long-read sequencing technologies to compare alternative mRNA splicing between the CD4 and CD8 T cell lineages. While long-read technology was effective at assembling full-length alternatively spliced transcripts, the low sequencing depth did not facilitate accurate quantitation. On the other hand, short-read technology was ineffective at assembling full-length transcripts but was highly accurate for quantifying expression. We show that integrating long-read and short-read data together achieves a more complete view of transcriptomic diversity. We found that while the overall usage of transcript isoforms was very similar between the CD4 and CD8 lineages, there were numerous alternative spliced mRNA isoforms that were preferentially used by one lineage over the other. These alternative spliced isoforms included ones with different exon usage, exon exclusion or intron inclusion, all of which are expected to significantly alter the protein sequence.